![]() ![]() A new folder can be created by entering a name in the text box, and then clicking the Create Folder icon. The entire list can be viewed by moving the scroll bar down.ĥ: New folders can be created by clicking on the Folder icon in the upper right corner of the pop-up window.Ħ: This will open a new pop-up window. Clicking on a folder will add it to the text box.ģ: New Folders can also be created by clicking on the folder icon at the end of the text box.Ĥ: This will open a pop-up window that shows all the folders that are available in the private workspace. Click the Add button at the end of the text box, and the genome will appear in the table.ĩ: To add a different type of genome (Reference, Representative, or All Other Public Genomes), click on the filter icon and click the check boxes to the desired category.ġ0: The selected genomes will be moved to the Selected Genome Input Table by clicking on the name and then the Add button.ġ: Several parameters must be addressed before the codon tree job can be submitted, and the Submit button will turn blue when the job is ready.Ģ: Clicking on the down arrow that follows the text box underneath Output Folder will show the folders that have most recently been created by the researcher. To add a private genome, click on the Filter icon at the beginning of the text box underneath Select Genome.Ģ: This will open a drop-down box with a list of the types of genomes that can be filtered onģ: Click off the check box in front of Reference, Representative and All Other Public Genomes to enable filtering on private genomes that are in the researcher’s workspace.Ĥ: Clicking on the drop-down box at the end of the text box under Select Genome will show the private genomes in the workspace that have most recently been annotated.ĥ: The list can also be filtered by beginning to type a name in the text box under Select Genome.Ħ: A genome of interest can be selected by double clicking on it.ħ: This will auto-fill the name of the genome into the text box.Ĩ: The genome needs to be added into the Selected Input Genome Table. Up to 100 genomes can be used in this service. #Using codoncode aligner for phylogenic tree download#The resulting newick file can be viewed in PATRIC, and we also suggest that researchers download it and view it in FigTree to generate a publication quality image.ġ: Public or private genomes that are in the PATRIC database can be used to build a phylogenetic tree. Support values are generated using 100 rounds of the “Rapid” bootstrapping option of RaxML. A concatenated alignment of all proteins and nucleotides were written to a phylip formatted file, and then a partitions file for RaxML is generated, describing the alignment in terms of the proteins and then the first, second and third codon positions. Protein sequences are aligned using MUSCLE, and the nucleotide coding gene sequences are aligned using the Codon_align function of BioPython. Both the protein (amino acid) and gene (nucleotide) sequences are used for each of the selected genes from the PGFams. This tutorial deals with the Codon Trees pipeline. The default is set for Codon Trees, which uses the amino acid and nucleotide sequences from defined number of PATRIC’s global Protein Families (PGFams), which are picked randomly, to build an alignment, and then generate a tree based on the differences within those selected sequences. PATRIC provides two separate pipelines ( Codon Trees or All Shared Proteins) for building phylogenetic trees. Searching for Features by Protein Family.Locating All Genomes for a Taxonomic Group.Locating the Phylogenetic Tree Service – Codon Tree App Building Phylogenetic Trees - Codon Trees.Submitting the Comprehensive Genome Analysis Job.Comparing Your New Genome to Existing Neighbors. ![]()
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